SMTL ID : 7szg.1

Structure of the Rieske Non-heme Iron Oxygenase GxtA Pressurized with Xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-trimer

Ligands

3 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.1: 7 residues within 4Å: Chain A: C.55, H.57, R.58, C.74, Y.76, H.77, W.79 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.55, A:H.57, A:C.74, A:H.77 FES.8: 7 residues within 4Å: Chain B: C.55, H.57, R.58, C.74, Y.76, H.77, W.79 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.55, B:H.57, B:C.74, B:H.77 FES.15: 7 residues within 4Å: Chain C: C.55, H.57, R.58, C.74, Y.76, H.77, W.79 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.55, C:H.57, C:C.74, C:H.77

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: V.162, F.165, P.166, L.173, G.174, A.179, V.181, Y.198, Q.199, V.200, H.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.162, A:A.179, A:H.201, A:H.201 GOL.3: 4 residues within 4Å: Chain A: E.248, R.291, T.330, V.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.248, A:R.291 GOL.9: 5 residues within 4Å: Chain B: T.3, E.248, R.291, T.330, Y.331 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.3, B:R.291 Water bridges: B:R.291 GOL.11: 4 residues within 4Å: Chain B: H.30, I.246, D.247, N.250 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.30, B:D.247 GOL.16: 3 residues within 4Å: Chain C: V.88, P.94, M.96 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.96 Water bridges: C:M.96 GOL.17: 3 residues within 4Å: Chain C: K.144, D.274, E.278 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.144, C:D.274, C:E.278 Water bridges: C:D.274, C:D.274

3 x FE: FE (III) ION(Non-covalent)

FE.4: 3 residues within 4Å: Chain A: H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.164, A:H.169, A:D.280, H2O.1, H2O.2 FE.12: 3 residues within 4Å: Chain B: H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.169, B:D.280, H2O.5, H2O.5 FE.18: 3 residues within 4Å: Chain C: H.164, H.169, D.280 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.164, C:H.169, C:D.280, H2O.7, H2O.9

3 x XE: XENON(Non-covalent)

XE.5: 2 residues within 4Å: Chain A: Y.273 Ligands: DTT.6 No protein-ligand interaction detected (PLIP) XE.13: 2 residues within 4Å: Chain B: Y.273 Ligands: DTT.10 No protein-ligand interaction detected (PLIP) XE.19: 1 residues within 4Å: Chain C: Y.273 No protein-ligand interaction detected (PLIP)

3 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.6: 4 residues within 4Å: Chain A: Q.226, C.228, D.239 Ligands: XE.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.239, A:Y.273 DTT.10: 5 residues within 4Å: Chain B: S.159, N.216, Q.226, C.228 Ligands: XE.13 No protein-ligand interaction detected (PLIP) DTT.20: 8 residues within 4Å: Chain C: S.159, L.173, N.216, Q.226, C.228, D.239, Y.255, Y.273 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.255, C:Y.255 Water bridges: C:S.159

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: W.12, H.222, L.224, C.225 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: R.219, L.220, S.221, H.222, C.225 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain C: S.41, H.42, N.69, N.70 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Design principles for site-selective hydroxylation by a Rieske oxygenase. Nat Commun (2022)

Release Date

2022-01-19

Peptides

SxtDIOX: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

SxtDIOX

Related Entries With Identical Sequence